Root beer continues to serve as a metaphor for the Federation in Quark's mind, as he wishes he could serve root beer again (despite finding it vile).
The hatch Rom is waiting to open to sabotage the Dominion's plan has the label "A51/Restricted area" on it. This is a reference to the famed Area 51 military base in southern Nevada. Area 51 was seen in Little Green Men (1995).
First appearance of an admiral uniform that now matches the new officer uniforms.
Nog presents Sisko with a bottle of Saurian brandy. This fictional libation first appeared in The Enemy Within (1966). The distinctive, curved "powder horn" bottle used in both series was fashioned from a commemorative bottle from the George Dickel whiskey distillery.